February 2004

February 2004

Editorial

This issue illustrates the breadth and dynamism of plant science. In the Technology section, we focus on a series of dazzling genome initiatives that have transformed the field (see p. 32). The Research section includes a story on the striking similarities between the innate immune mechanisms of plants and animals; another on the structure of a molecular complex at the heart of photosynthesis; and a third on the catastrophic impact of recent wildfires on forest ecosystems (see pp. 26, 25, and 23

Opinion

Nanoscience and nanotechnology are among today's most promising fields of research. If their full potential is to be realized, we need to attend along the way to key ethical issues. But ethics should not be grounded in exaggerations, either positive or negative; hype just obscures important issues.One type of hype comes from enthusiasts who argue that nanotech is a wonderful thing. One day, they aver, "nanoassemblers" will convert coal into diamonds, turn grass clippings into beef, and restore t

Letter

Well done.1 I bet a lot of folks are echoing Oscar Wilde and saying, "I wish I'd written that."Andrew T. Lloyd, PhDGenetics Department Trinity College, Dublin atlloyd@tcd.ieElvis BLAST search is some fundamental research that needed to be done.1 I am still left to wonder if the DEVIL (Asp-Glu-Val-Ile-Leu) can be associated with some type of gene jumping into the chomosomes of today's terrorists?Paul DutchakMSc CandidateDepartment of Biochemistry University of Saskatchewan edbrock@hotmail.com

We have noticed a disregard for the appropriate use of the word "first" in scientific articles in the past year. While there is certainly some prestige with being the first author(s) to describe a new scientific finding or unusual clinical entity, invoking this distinction should be done only after a thorough and meticulous literature search warrants it and only when such a claim of priority has some relevance of importance.For example, one paper described the first reportedly successful implant

Though I have been retired for many years as a photosynthesis researcher, some of J. Craig Venter's statements in his article 1 did not compute with my understanding of evolution and the photosynthetic process.Venter asserted that Methanococcus jannaschii gets its energy from "hydrogen electrons." Even in deep-sea vents, I doubt that there are hydrogen electrons floating around loose. I suspect the source is hydrogen sulfide or one or more other highly reduced inorganic molecules.Venter also sta

Although English is not my mother tongue, I am very concerned by the subject.1 As an editor of microbiological periodicals, I had [the need] sometimes to reject manuscripts of native English speakers because of poor grammar. French is under siege, too. For example, the new generation of Quebec scientists is often ignorant of basic principles of French grammar and even spelling.I am a virologist and a specialist of bacterial viruses. What galls me particularly is the increasing use of "bacterioph

Snapshot

Under what conditions should GM crops be deployed?Readers rank the importance of their objectionsGM crops may cause environmental disruption, 63%.Developing GM crops could solidify the control that a few large corporations have on agriculture, 59%.Consuming GM crops may create unrecognized hazards to human health, 39%.Creating transgenic animals and plants is ethically wrong, 10%.Of the 302 readers who responded, nearly 100 of them commented passionately on this subject. You can see some of thei

5-Prime

What are circadian rhythms?These timing systems dictate when plants will bloom, force people to fall asleep at their desks, urge birds to fly south, and influence a host of other activities. While circadian rhythms run on a 24-hour clock, others also exist, including tidal, lunar, and annual rhythms.Which organisms have them?A lot; from bread molds to humans. Well-studied rhythms include those in cyanobacteria, the bread mold Neurospora crassa, rice, Arabidopsis, fruit flies, mice, Syrian hamste

Frontlines

Courtesy of CSHLWere you late getting that Valentine's Day gift? Not to fret: Buy double helix jewelry for your molecular biologist sweetheart. Cathy Cyphers Soref, a fundraiser for Cold Spring Harbor Laboratory (CSHL), says the double helix is "as universal a symbol as the heart." And it looks just as lovely in diamonds.Soref has opened a store to benefit CSHL, called DNA Stuff http://www.DNAStuff.com. It sells DNA-themed items including jewelry and denim clothing that puns on "gene/jean." The

Courtesy of Martin Lockey, University of ColoradoIt's a slab of rock, two-by-two feet square, which tells a 75-million-year-old story. Imprinted in one part is a footprint indentation (below the coin) of a tiny mammal and the impressions of a leaf; on another part are marks typically left by raindrops."It looks like the animal took cover underneath some type of leaf that protected the surface from raindrops," says Martin Lockley, University of Colorado, Denver, who discovered the fossilized trac

First Person

Courtesy of Scripps Research InstituteIf he weren't so young, the moniker "Father Time" might fit geneticist Steve A. Kay quite well. At 44, the man whose lab determined how flowers know when to bloom is admittedly obsessed with clocks, whether they go off in Arabidopsis, Drosophila, or the mouse. The fascination began after he helped discover the cab gene in the early 1980s as a postdoc at Rockefeller University. "These circadian rhythms were doing a lot to me," he says in his characteristic, t

Foundations

Courtesy of David McKay, NASAIt weighs only 1.9 kilograms and is an estimated 4.5 billion years old. Yet the ALH84001 meteorite is probably the most argued-about rock in the universe (or at least in our solar system.) The anonymous member of an Antarctic geological field survey who found the rock in 1984 wrote in the field ticket's margins, "Yawza yawza!" Twenty years later, scientists are still making exclamations about the rock's innards. Some suspect that the ghostly forms in this scanning el

Feature

Give a postdoc an environment that encourages collegial work, and not competitive strife, and that person will respond with ample praise. At least, that's the lesson of The Scientist's Best Places for Postdocs 2004 survey; it's the magazine's largest yet, with 3,529 usable responses from postdoctoral researchers in Western Europe, Canada, and the United States.Postdocs rated access to publications and journals as the most important attribute of a university. High-quality research tools attracted

Institutions that nurture postdocs' scientific development dominated this year's Best Places for Postdocs survey. Participants ranked five federally funded research facilities among the top 15 institutions, all of which earned high marks for scientific development and resources.US government labs have become fertile greenhouses for some of the country's best and brightest researchers. Because government labs also dole out grants to institutions and scholars, they have become exemplars for other

The University of Alberta's pre-eminence in The Scientist's postdoc survey came as little surprise to many of the institution's researchers. These scientists cited as particularly important the April 2003 opening of a campus postdoc office, which provides a wide range of training and support services. The new office has encouraged postdocs to attend sessions on teaching, communication, and leadership, with which science graduates all too often lack experience, says postdoc Sheryl Gares.Carlos Fl

Research

While the most obvious components of a forest ecosystem are above ground, perhaps the most essential elements are found below the surface. Forest soils are home to millions of microorganisms, such as molds, fungi, algae, cyanobacteria, rotifers, and protozoa, and larger soil invertebrates, including mites, snails, slugs, centipedes, spiders, nematodes, earthworms, and springtails. These perform physical and biological processes needed for a healthy ecosystem, including nutrient recycling, waste

Courtesy of Robert FaustWildfires destroyed more than 3,600 homes and 750,000 acres of southern California's chaparral forests in 2003. Although these ecosystems are adapted to frequent, low-intensity burns, many ecologists say that fuel-load buildup due to years of fire suppression has led to catastrophic blazes. Brent Roath, a soil scientist stationed at the Sierra National Forest, says that once a fire is extinguished, assessing the damage and implementing necessary treatments "can take weeks

In a study that could offer a glimpse into sleep's still poorly understood functions, researchers have identified genes upregulated specifically during sleep.1 The findings contain surprises, investigators say. One is simply that there are many such genes, at least as many as are turned on while awake, belying the common-sense view that sleep implies inactivity. Another is that the sleep-related changes in gene expression extend to the cerebellum, a structure not previously known to participate

PSII REFINED:Helices are represented as cylinders. Chlorophylls of the D1/D2 reaction center are light green, pheophytins are blue. Chlorophylls of the antenna complexes are dark green, β-carotenes are in orange, hemes are in red. The oxygen evolving center (OEC) is shown as the red, magenta, and cyan balls representing oxygen atoms, Mn ions, and Ca2+ respectively.The planet's most prolific atmospheric oxygen source has just given up its most detailed mug shot yet. Jim Barber, a professor a

As life's diversity demonstrates, nature has a pretty large toolbox for designing adaptations. While in many ways an efficient builder, it often reuses blueprints, even if not starting with the same tools. Analogous wing structures in bird and bat suggest a why-mess-with-success ethos. New World cacti and desert-dwelling Euphorbiaceae in the Old World share protective spines and photosynthesizing stems even though the last common ancestor predates such modifications.Beyond structural adaptations

Hot Paper

EYE CANDY:Courtesy of Greg Suh, University of California Los Angeles, Andrew Moore, InfrancoMoore GroupThis developing eye from a chimeric Drosophila has wild-type tissue at the top and csn5 mutant tissue at the bottom causing disorganization. Overlaid is a schematic showing the predicted metalloprotease site of CSN5 cleaving an isopeptide bond.It doesn't take a green thumb to predict what happens to plants left in the dark: They wither. But in the late 1980s and early 1990s, researchers, includ

James King-Holmes/Science Photo LibraryIn the world of life-extending therapies, a lobotomy doesn't sound like an attractive option, but for the nematode Caenorhabditis elegans, destruction of particular sensory neurons can extend, or reduce, lifespan by as much as 30%. Joy Alcedo and Cynthia Kenyon at the University of California, San Francisco, have used a laser to kill individual neurons; they suggest that what may be happening to modify the lifespan of worms may also be at play in higher org

Courtesy Sidarta RibeiroSleep, to the joy of nappers everywhere, appears to be a building time for memories. Researchers at the Duke University Medical Center successfully recorded the electric signature of individual neurons firing during the two types of sleep, slow-wave sleep and rapid eye movement (REM) sleep.The team, led by postdoc Sidarta Ribeiro, implanted microscale probes into rat forebrain to determine the firing patterns of individual neurons "resonating" with recently captured memor

Software Watch

Biological databases are everywhere. From protein libraries in Switzerland to genome repositories in Maryland, one could spend hours tracking down all the sources of information on the Internet. An ambitious new project at the San Diego Supercomputer Center, University of California, aims to bring them all into one easy-to-use, centrally hosted place that is open to all.Culling data from over a dozen databases, the Encyclopedia of Life project (EOL, http://eol.sdsc.edu/) seeks "to catalog the co

Patent Watch

Courtesy of Henry DaniellGenetically engineered plants pose several major environmental concerns, according to Henry Daniell, a professor of molecular biology and microbiology at the University of Central Florida. When foreign genes are introduced into the nuclear genome, they end up in pollen, posing the risk of transfer to other species. And sometimes, expression levels are low.Daniell and colleagues have come up with what he says is a solution: chloroplast genetic engineering. The method R

Gadget Watch

Courtesy of TechnikaImpatient molecular biologists who need to know – now! – if their gels are done, have a new, pen-sized ally. Rather than carrying their gel trays to the dark room, they can whip out the diminutive UV Light Pen ($17, US), from Technika, for on-the-spot gel analysis.The light pen uses LED (light-emitting diode) technology. Instead of filaments, LEDs use low-power semiconductor chips. As a result, the Light Pen "virtually uses no electricity, so the batteries last a

Technology

FOCUS ON TECHNOLOGY:Courtesy of Lynx TechnologiesBy conscious design, plant genomics initiatives have devoted initial resources to new technology development. Part of that money went to developing functional genomics approaches, and part to new sequencing technologies. Lynx's Massively Parallel Signature Sequencing (MPSS) approach, shown here, can decipher millions of sequence fragments – each represented by one bead in this image – simultaneously.Plants are quieter than people. They

Courtesy of QiagenLooking for a way to isolate a nucleic acid and don't know where to start? The availability of options is the least of your worries. Whatever your particular sample source, throughput requirement, or scale, odds are good that somebody has a system available to help.The sea of options is vast, and lucrative. Analysts predict that the rapidly growing nucleic acid isolation market may generate revenues reaching nearly $500 million by 2009.1 According to Frost & Sullivan, a mar

ABI 8500 Affinity Chip AnalyzerCourtesy of Applied BiosystemsFor labs equipped to measure surface plasmon resonance (SPR), determining how biomolecules interact with each other is simple. Load a glass slide into the benchtop instrument, give it some tubes, click the mouse a few times, and voila! – out come affinity measurements, on-rates, off-rates, and dissociation constants, all in real time."We can absolutely determine affinity, concentration, and all other things," says Stefan Lofas, v

Courtesy of GenovoxxIn the ever-growing field of new DNA sequencing methods, it's a single-molecule world. By far the bulk of recent efforts to develop cheaper, faster genomic sequencing techniques have analyzed individual rather than populations of DNA molecules.One of the latest contenders is Lübeck, Germany-based Genovoxx's AnyGene™ method http://www.genovoxx.de, in which DNA fragments deposited on a two-dimensional array are subjected to sequencing-by-synthesis. Labeled nucleotide

Stratagene of La Jolla, Calif. http://www.stratagene.com, recently introduced its new Biotrek reagent which shuttles whole proteins into cells. The protein of interest is mixed with a lipid carrier to form noncovalent complexes, which then attach to negatively charged surfaces of the plasma membrane and enter the cell via fusion or endocytosis. Once inside, the complexes disassemble rapidly, releasing active protein into the cell."You can often see an effect within 10 minutes," compared to tradi

BD Biosciences-Clontech of Palo Alto, Calif., http://www.clontech.com has harnessed the power of a DNAzyme, the DNA equivalent of a ribozyme, in its new BD QZyme™ assay for quantitative PCR. The sensitive system, which can detect fewer than 10 copies of a target, can be used with any real-time thermocycler and works via a simple amplification and cleavage reaction.Appended to the gene-specific 5' PCR primer is the inactive antisense strand of a phosphodiesterase DNAzyme. As double-stranded

Tip Trove

Courtesy of Claudina Aleman StevensonPostdoctoral Associations (PDAs) provide a clear voice for postdocs brought together by an issue, and they can solve real problems. Start a postdoc association as a collaboration; identify allies in seemingly unlikely places (faculty, administrators, and in the Dean's Office). Remaining positive and supportive builds and sustains momentum.- Claudina Aleman Stevenson, PhD, is a visiting scientist from NCI at Tufts University School of Medicine, Boston; and cha

Moonlighting

Courtesy of Monica MarcuMonica Marcu's life outside the lab is just that: outside. As a nature photographer, she spends her free time, "all the weekends, all the holidays," exploring the parks and nature preserves in and around the Washington, DC area.After years of taking her camera along on hikes, her husband suggested: Why not be a photographer? Inspired, Marcu set about reading books and taking classes; she studied with professionals and practiced on her own. In time, her technique and her c

Data Points

National Science FoundationCompiled by Francesco FiondellaPostdoctoral support on NSF research grants, in millions of dollarsUK Research CouncilsTotal amount of postdoctoral fellowships given by the MRC, in millions of pounds†† Includes funding for both clinical and basic researchGrants given to postdocs by the BBSRC, in millions of pounds††††Not all disciplines shownNote: One British pound equalled $1.82 on Jan. 29Sources: National Science Foundation; Medical

Profession

Elias Zerhouni listens to the gripes at his third town hall meeting with employees since becoming director of the National Institutes of Health nearly two years ago. The Bethesda, Md., campus lacks adequate parking. The new computer system is a mess. The parking lots are too dark.Zerhouni shares his problems, too. Congress wants him to explain why government scientists are earning millions in fees and stock options from private firms. The agency remains on edge as its the nation's first line of

Last summer, a member of the biology department of the University of Udine in Italy approached Nicola Vitacolonna with an intriguing project. The ANREP program, which annotates structural motifs in gene or protein sequences, was out of date having been written more than a decade ago. Although still used by molecular biologists, its slow computing ability meant a straightforward multiple search could take all night on a desktop PC. The Udine biologist wanted Vitacolonna, a postdoctoral fellow in

Postdoc Talk

Strange smells, weird lighting, people with serious expressions on their faces as they quietly work on their research. Sound like the lab? Maybe. But I'm talking about the library, a place I have recently rediscovered. Not the online searchable library, not the downloadable PDF file library, but the real library. You know the place. It's that old, familiar building full of books and journals, 1970s-style study carrels, and the constant hum of photocopiers.My story starts here: I know a lot about

Science Rules

The British Parliament will this year pass a revised Human Tissue Act, prompted by a series of incidents in which hospitals retained children's organs without their parents' permission. According to the new law, scientists will have to obtain informed consent when using human organs or tissues for their research.The new regulations will bring legal certainty to British scientists, but across Europe, they only add to the crosshatch of conflicting rules regarding the use of human materials. A few

Closing Bell

Would popping daily citaloprams, I wonder, have restrained Jackie Kennedy's celebrated spending sprees and prevented the purported ensuing marital discord? How about a fluvoxamine prescription? Or natrexone? And what about publisher William Randolph Hearst who, at the peak of his purchasing power in the 1920s, spent $15 million a year? Even after achieving near bankruptcy, Hearst continued feeding his mania for antiquities, tapestries, oriental rugs, paintings, and other collectibles. Would medd